TargetingModel-class: S4 class defining a targeting model
Description
TargetingModel defines a common data structure for mutability, substitution and
targeting of immunoglobulin (Ig) sequencing data in a 5-mer microsequence context.
Slots
name- Name of the model.
description- Description of the model and its source data.
species- Genus and species of the source sequencing data.
date- Date the model was built.
citation- Publication source.
substitution- Normalized rates of the center nucleotide of a given 5-mer
mutating to a different nucleotide. The substitution model
is stored as a 5x3125 matrix of rates. Rows define
the mutated nucleotide at the center of each 5-mer, one of
c("A", "C", "G", "T", "N"), and columns define the
complete 5-mer of the unmutated nucleotide sequence. mutability- Normalized rates of a given 5-mer being mutated. The
mutability model is stored as a numeric vector of length 3125
with mutability rates for each 5-mer.
targeting- Rate matrix of a given mutation ocurring, defined as
$mutability * substitution$. The targeting model
is stored as a 5x3125 matrix. Rows define
the mutated nucleotide at the center of each 5-mer, one of
c("A", "C", "G", "T", "N"), and columns define the complete 5-mer
of the unmutated nucleotide sequence.